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Title: Dead simple OWL design patterns

Abstract

Bio-ontologies typically require multiple axes of classification to support the needs of their users. Development of such ontologies can only be made scalable and sustainable by the use of inference to automate classification via consistent patterns of axiomatization. Many bio-ontologies originating in OBO or OWL follow this approach. These patterns need to be documented in a form that requires minimal expertise to understand and edit and that can be validated and applied using any of the various programmatic approaches to working with OWL ontologies. We describe a system, Dead Simple OWL Design Patterns (DOS-DPs), which fulfills these requirements, illustrating the system with examples from the Gene Ontology. In conclusion, the rapid adoption of DOS-DPs by multiple ontology development projects illustrates both the ease-of use and the pressing need for the simple design pattern system we have developed.

Authors:
ORCiD logo [1];  [1];  [2];  [3]
  1. European Bioinformatics Inst. (EMBL-EBI), Cambridge (United Kingdom)
  2. RTI International, Research Triangle Park, NC (United States)
  3. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Genomics Division
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22); National Institutes of Health (NIH)
OSTI Identifier:
1379883
Grant/Contract Number:  
AC02-05CH11231; 58U41HG002273-14; U01 HG009453
Resource Type:
Accepted Manuscript
Journal Name:
Journal of Biomedical Semantics
Additional Journal Information:
Journal Volume: 8; Journal Issue: 1; Journal ID: ISSN 2041-1480
Publisher:
BioMed Central
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 60 APPLIED LIFE SCIENCES; OWL; OBO; design pattern

Citation Formats

Osumi-Sutherland, David, Courtot, Melanie, Balhoff, James P., and Mungall, Christopher. Dead simple OWL design patterns. United States: N. p., 2017. Web. doi:10.1186/s13326-017-0126-0.
Osumi-Sutherland, David, Courtot, Melanie, Balhoff, James P., & Mungall, Christopher. Dead simple OWL design patterns. United States. doi:10.1186/s13326-017-0126-0.
Osumi-Sutherland, David, Courtot, Melanie, Balhoff, James P., and Mungall, Christopher. Mon . "Dead simple OWL design patterns". United States. doi:10.1186/s13326-017-0126-0. https://www.osti.gov/servlets/purl/1379883.
@article{osti_1379883,
title = {Dead simple OWL design patterns},
author = {Osumi-Sutherland, David and Courtot, Melanie and Balhoff, James P. and Mungall, Christopher},
abstractNote = {Bio-ontologies typically require multiple axes of classification to support the needs of their users. Development of such ontologies can only be made scalable and sustainable by the use of inference to automate classification via consistent patterns of axiomatization. Many bio-ontologies originating in OBO or OWL follow this approach. These patterns need to be documented in a form that requires minimal expertise to understand and edit and that can be validated and applied using any of the various programmatic approaches to working with OWL ontologies. We describe a system, Dead Simple OWL Design Patterns (DOS-DPs), which fulfills these requirements, illustrating the system with examples from the Gene Ontology. In conclusion, the rapid adoption of DOS-DPs by multiple ontology development projects illustrates both the ease-of use and the pressing need for the simple design pattern system we have developed.},
doi = {10.1186/s13326-017-0126-0},
journal = {Journal of Biomedical Semantics},
number = 1,
volume = 8,
place = {United States},
year = {2017},
month = {6}
}

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Works referenced in this record:

Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles
journal, September 2005

  • Subramanian, A.; Tamayo, P.; Mootha, V. K.
  • Proceedings of the National Academy of Sciences, Vol. 102, Issue 43, p. 15545-15550
  • DOI: 10.1073/pnas.0506580102